[English] 日本語
Yorodumi
- PDB-8ytg: Crystal structures of human IRF2BP2 RING domain in complex with I... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ytg
TitleCrystal structures of human IRF2BP2 RING domain in complex with IRF2 peptide
Components
  • Interferon regulatory factor 2
  • Interferon regulatory factor 2-binding protein 2
KeywordsTRANSCRIPTION / IRF2BP2 / RING domain / IRF2
Function / homology
Function and homology information


immature B cell differentiation / immune system process / Pyroptosis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Interferon gamma signaling / transcription corepressor activity / sequence-specific double-stranded DNA binding / Interferon alpha/beta signaling / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription activator activity, RNA polymerase II-specific ...immature B cell differentiation / immune system process / Pyroptosis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Interferon gamma signaling / transcription corepressor activity / sequence-specific double-stranded DNA binding / Interferon alpha/beta signaling / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription activator activity, RNA polymerase II-specific / defense response to virus / cell population proliferation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / focal adhesion / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Interferon regulatory factor 2-binding protein 1 & 2, zinc finger / Interferon regulatory factor 2-binding protein 1/2, C3HC4-type RING finger superfamily / Interferon regulatory factor 2-binding protein zinc finger / Interferon regulatory factor-1/2 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. ...Interferon regulatory factor 2-binding protein 1 & 2, zinc finger / Interferon regulatory factor 2-binding protein 1/2, C3HC4-type RING finger superfamily / Interferon regulatory factor 2-binding protein zinc finger / Interferon regulatory factor-1/2 / Interferon regulatory factor, conserved site / IRF tryptophan pentad repeat DNA-binding domain signature. / Interferon regulatory factor transcription factor / interferon regulatory factor / Interferon regulatory factor DNA-binding domain / IRF tryptophan pentad repeat DNA-binding domain profile. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Interferon regulatory factor 2 / Interferon regulatory factor 2-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsWang, G.C. / Ding, J.P.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030305 China
CitationJournal: Nat Commun / Year: 2024
Title: IRF2BP2 binds to a conserved RxSVI motif of protein partners and regulates megakaryocytic differentiation.
Authors: Wang, G. / Lu, T. / Zhang, L. / Ding, J.
History
DepositionMar 25, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Interferon regulatory factor 2-binding protein 2
B: Interferon regulatory factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,9685
Polymers9,7722
Non-polymers1963
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-37 kcal/mol
Surface area5060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.733, 39.868, 36.247
Angle α, β, γ (deg.)90.00, 108.21, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Interferon regulatory factor 2-binding protein 2 / IRF-2-binding protein 2 / IRF-2BP2


Mass: 8867.110 Da / Num. of mol.: 1 / Fragment: RING domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IRF2BP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z5L9
#2: Protein/peptide Interferon regulatory factor 2 / IRF-2


Mass: 905.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P14316
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.5 M ammonium sulfate and 0.1 M sodium acetate (pH 4.6)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.45→39.87 Å / Num. obs: 12812 / % possible obs: 98.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 10.3
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1270

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
DIALSdata scaling
DIALSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→34.43 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1887 625 4.89 %
Rwork0.1649 --
obs0.1661 12782 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms621 0 3 158 782
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006636
X-RAY DIFFRACTIONf_angle_d0.873860
X-RAY DIFFRACTIONf_dihedral_angle_d5.31185
X-RAY DIFFRACTIONf_chiral_restr0.09394
X-RAY DIFFRACTIONf_plane_restr0.01112
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.60.20071700.17033010X-RAY DIFFRACTION99
1.6-1.830.17551630.15163035X-RAY DIFFRACTION100
1.83-2.30.19761510.1663059X-RAY DIFFRACTION99
2.3-34.430.18421410.16773053X-RAY DIFFRACTION97

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more